Systems for enhancing target mrna expression and uses thereof

Abstract

Provided herein are nucleic acid agents that are or comprise one or more nucleic acid molecules, together comprising (a) a complementary element that hybridizes with a target mRNA; and (b) a poly(A) element. In some embodiments, the target mRNA is an mRNA of an active allele of a gene associated with a disorder associated with a decrease in the expression of a protein from the mRNA, wherein the disorder is a haploinsufficiency disorder.

What is claimed is: 
     
         1 . A nucleic acid agent comprising:
 (a) a complementary element that hybridizes with a target mRNA; and   (b) a poly(A) element.   
     
     
         2 . The nucleic acid element of  claim 1 , wherein the complementary element hybridizes to a 3′ untranslated element of the target mRNA. 
     
     
         3 . The nucleic acid agent of  claim 1 or 2 , wherein the complementary element comprises RNA or DNA. 
     
     
         4 . The nucleic acid agent of any one of  claims 1-3 , wherein the poly(A) element is located 5′ to the complementary element. 
     
     
         5 . The nucleic acid agent of any one of  claims 1-4 , wherein the poly(A) element is located 3′ to the complementary element. 
     
     
         6 . The nucleic acid agent of  claim 5 , wherein the poly(A) element is located 3′ to the complementary element and the nucleic acid agent further comprises a 5′ cap element located 5′ to the complementary element. 
     
     
         7 . The nucleic acid agent of any one of  claims 1-6 , wherein the nucleic acid agent comprises a first poly(A) element located 5′ to the complementary element and a second poly(A) element located 3′ to the complementary element. 
     
     
         8 . The nucleic acid agent of any one of  claims 1-7 , wherein the poly(A) element comprises about 20 nucleotides. 
     
     
         9 . The nucleic acid agent of any one of  claims 1-7 , wherein the poly(A) element comprises about 50 nucleotides. 
     
     
         10 . The nucleic acid agent of any one of  claims 1-7 , wherein the poly(A) element comprises about 75 nucleotides. 
     
     
         11 . The nucleic acid agent of any one of  claims 1-10 , wherein the nucleic acid agent further comprises a nucleotide modification. 
     
     
         12 . The nucleic acid agent of  claim 11 , wherein the nucleotide modification is a N 1 -methyladenosine (m 1 A), N 6 -methyladenosine (m 6 A), or adenosine to inosine (A-to-I) modification. 
     
     
         13 . The nucleic acid agent of  claim 11 , wherein the nucleotide modification is a pseudouracil, M1-pseudouracil, 5-methoxyuridine (5moU), or N4-acetylcytidine modification. 
     
     
         14 . The nucleic acid agent of any one of  claims 1-13 , wherein the nucleic acid agent is encoded by a sequence that comprises or consists of SEQ ID NO: 2 or SEQ ID NO: 3, or a sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 2 or SEQ ID NO: 3. 
     
     
         15 . The nucleic acid agent of any one of  claims 1-14 , wherein the target mRNA is an mRNA of an active allele of a gene associated with a disorder associated with a decrease in the expression of a protein from the mRNA. 
     
     
         16 . The nucleic acid agent of  claim 15 , wherein the disorder is a haploinsufficiency disorder. 
     
     
         17 . The nucleic acid agent of  claim 15 or 16 , wherein the target mRNA encodes the MeCP2 protein. 
     
     
         18 . The nucleic acid agent of  claim 17 , wherein the complementary element comprises or consists of SEQ ID NO: 1. 
     
     
         19 . A recombinant expression system comprising a nucleic acid sequence encoding a nucleic acid agent comprising (i) a complementary element that hybridizes with a target mRNA and (ii) a poly(A) element. 
     
     
         20 . The recombinant expression system of  claim 19 , wherein the complementary element hybridizes to a 3′ untranslated element of the target mRNA. 
     
     
         21 . The recombinant expression system of  claim 19 or 20 , wherein the complementary element comprises RNA or DNA. 
     
     
         22 . The recombinant expression system of any one of  claims 19-21 , wherein the poly(A) element is located 5′ to the complementary element. 
     
     
         23 . The recombinant expression system of any one of  claims 19-22 , wherein the poly(A) element is located 3′ to the complementary element. 
     
     
         24 . The recombinant expression system of  claim 23 , wherein the poly(A) element is located 3′ to the complementary element and wherein the RNA molecule further comprises a 5′ cap element located 5′ to the complementary element. 
     
     
         25 . The recombinant expression system of any one of  claims 19-24 , the nucleic acid molecule comprises a first poly(A) element located 5′ to the complementary element and a second poly(A) element located 3′ to the complementary element. 
     
     
         26 . The recombinant expression system of any one of  claims 19-25 , wherein the poly(A) element comprises about 20 nucleotides. 
     
     
         27 . The recombinant expression system of any one of  claims 19-25 , wherein the poly(A) element comprises about 50 nucleotides. 
     
     
         28 . The recombinant expression system of any one of  claims 19-25 , wherein the poly(A) element comprises about 75 nucleotides. 
     
     
         29 . The recombinant expression system of any one of  claims 19-28 , wherein the nucleic acid agent further comprises a nucleotide modification. 
     
     
         30 . The recombinant expression system of  claim 29 , wherein the nucleotide modification is a N 1 -methyladenosine (m 1 A), N 6 -methyladenosine (m 6 A), or adenosine to inosine (A-to-I) modification. 
     
     
         31 . The recombinant expression system of  claim 29 , wherein the nucleotide modification is a pseudouracil, M1-pseudouracil, 5-methoxyuridine (5moU), or N4-acetylcytidine modification. 
     
     
         32 . The recombinant expression system of any one of  claims 19-31 , wherein the recombinant expression system is encoded by a sequence that comprises or consists of SEQ ID NO: 2 or SEQ ID NO: 3, or a sequence that has at least 80%, at least 85%, at least 90%, at least 95%, or at least 99% sequence identity to SEQ ID NO: 2 or SEQ ID NO: 3. 
     
     
         33 . The recombinant expression system of any one of  claims 19-32 , wherein the target mRNA is an mRNA of an active allele of a gene associated with a disorder associated with a decrease in the expression of a protein from the mRNA. 
     
     
         34 . The recombinant expression system of  claim 33 , wherein the disorder is a haploinsufficiency disorder. 
     
     
         35 . The recombinant expression system of  claim 33 or 34 , wherein the target mRNA encodes the MeCP2 protein. 
     
     
         36 . The recombinant expression system  claim 35 , wherein the nucleic acid agent is or comprises a nucleic acid molecule that comprises or consists of SEQ ID NO: 1. 
     
     
         37 . An expression vector comprising the recombinant expression system of any one of  claims 19-36 . 
     
     
         38 . The expression vector of  claim 37 , wherein the expression vector is a viral vector. 
     
     
         39 . The expression vector of  claim 38 , wherein the viral vector is an adeno-associated viral vector (AAV), a lentiviral vector, or an adenoviral vector. 
     
     
         40 . A pharmaceutical composition that comprises or delivers the nucleic acid agent of any one of  claims 1-18 , the recombinant expression system of any one of  claims 19-36 , or the expression vector of any one of  claims 37-39 . 
     
     
         41 . A method of treating a haploinsufficiency disorder in a subject, the method comprising: administering to the subject a therapeutically effective amount of the pharmaceutical composition of  claim 40 . 
     
     
         42 . The method of  claim 41 , wherein the therapeutically effective amount of the pharmaceutical composition enhances the target mRNA protein expression. 
     
     
         43 . The method of  claim 41 or 42 , wherein the haploinsufficiency disorder is selected from the group consisting from 5qsyndrome, Adams-Oliver syndrome 1, Adams-Oliver syndrome 3, Adams-Oliver syndrome 5, Adams-Oliver syndrome 6, Alagille syndrome 1, Autoimmune lymphoproliferative syndrome type IA, Autoimmune lymphoproliferative syndrome type V, Autosomal dominant deafness-2A, Brain malformations with or without urinary tract defects (BRMUTD), Carney complex type 1, CHARGE syndrome, Cleidocranial dysplasia, Currarino syndrome, Denys-Drash syndrome/Frasier syndrome, Developmental delay, intellectual disability, obesity, and dysmorphic features (DIDOD), DiGeorge syndrome (TBXI-associated), Dravet syndrome, Duane-radial raysyndrome, Ehlers-Danlos syndrome (classic-like), Ehlers-Danlos syndrome (vascular type), Feingold syndrome 1, Frontotemporal lobar degeneration with TDP43 inclusions (FTLD-TDP), GRN-related, GLUT I deficiency syndrome, Greig cephalopolysyndactyly syndrome, Hereditary hemorrhagic telangiectasia type 1, Holoprosencephaly 3, Holoprosencephaly 4, Holoprosencephaly 5, Holt-Oram syndrome, Hypoparathyroidism, sensorineural deafness, andrenal disease (HDR), Kleefstra syndrome 1, Klippel-Trenaunay syndrome (AAGF-related), Leri-Weill dyschondrosteosis, Marfan syndrome, Mental retardation and distinctive facial features with or without cardiac defects (MRFACD), Mental retardation, autosomal dominant 1, Mental retardation, autosomal dominant 19, Mental retardation, autosomal dominant 29, Nail-patella syndrome (NPS), Phelan-McDermid syndrome, Pitt-Hopkins syndrome, Primary pulmonary hypertension 1, Rett syndrome (congenital variant), Smith-Magenis syndrome (RAII associated), Sotos syndrome 1, Sotos syndrome 2, Stickler syndrome type I, Supravalvular aorticstenosis, SYNGAPI-related intellectual disability, Treacher Collins syndrome, Trichorhinophalangeal syndrome type I, Ulnar-mammary syndrome, van der Woude syndrome1, Waardenburg syndrome type 1, Waardenburg syndrome type 2A, and Waardenburg syndrometype 4C. 
     
     
         44 . The method of any one of  claims 41-43 , wherein the subject is a mammal. 
     
     
         45 . The method of  claim 44 , wherein the subject is a human.